Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A5 F178 I0 R1	41	49.4	1100758	95.6%	1052324	140.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,646,189	G→C	100%	A155G (GCA→GGA)	ypdF ←	Aminopeptidase YpdF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,646,189	0	G	C	100.0%	105.2 / ‑6.5	34	A155G (GCA→GGA)	ypdF	Aminopeptidase YpdF
Reads supporting (aligned to +/- strand): ref base G (0/0); major base C (17/16); minor base T (0/1); total (17/17)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGATATACG  >  USA300TCH1516_ALE/1646057‑1646325

tcccTTGCAACACCATGGGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTCGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTGTCAGTCATGCCTCCTTTTac                                                                                                                                   <  2:39928/137‑1 (MQ=255)

  aCTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTacaa                                                                                                                                 <  1:70368/140‑1 (MQ=255)

          cgccATGTGGGAAAGCATCTCTATTACCAGATTCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTATCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTaaa                                                                                                                         <  1:477414/138‑1 (MQ=255)

           acCATGTTGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTaaaa                                                                                                                        <  1:448893/140‑1 (MQ=255)

             cATGTTGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAata                                                                                                                      <  1:225068/140‑1 (MQ=255)

               tgtgGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTATAATATTGCCATTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAatata                                                                                                                    >  1:110930/1‑140 (MQ=255)

               tgtgATAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAatata                                                                                                                    >  1:376161/1‑140 (MQ=255)

                          atctctATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGttt                                                                                                         <  2:1879/138‑1 (MQ=255)

                             tctATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAGATATATTCATATGTTtcat                                                                                                      <  1:410043/140‑1 (MQ=255)

                                        aTGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTa                                                                                           <  1:232486/140‑1 (MQ=255)

                                         tGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTATTACAACAGTTAAAATATATTCATATGATACATCAACAATATTAg                                                                                          >  1:219622/1‑140 (MQ=255)

                                          gCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAgc                                                                                         >  1:153793/1‑140 (MQ=255)

                                           cTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATCTTAgct                                                                                        >  2:491089/1‑140 (MQ=255)

                                                       cGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAAtt                                                                            >  2:515499/1‑140 (MQ=255)

                                                          atgatgGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTCTCAGTCATGTCTCCTTTTACAACAGTTAAAATATATTCATATGTTTTATTAACATTATTAGCTGCTTTTTGAATTaaa                                                                         >  2:457660/1‑140 (MQ=255)

                                                               ggTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTTCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAATTATATTCATATGTTTCATCCACAATATTAGATGCTTTTTGAATTAAAGCAAt                                                                    >  2:289195/1‑140 (MQ=255)

                                                                gTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATCTTAGCTGCTTTTTGAATTAAAGCAAtt                                                                   >  2:274467/1‑140 (MQ=255)

                                                                            cTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCATCAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCt                                                       <  2:301209/140‑1 (MQ=255)

                                                                            cTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAACATCt                                                       <  2:69100/140‑1 (MQ=255)

                                                                               aTTCTAGCATTTTGCTTTCTAATATTGCCTTTGATTCTTTTTCAGTCACGCCTCCTTTTACAACCGTTAAAATATATTGATACGTTTCATCAACAATATTTGCTTCTTTTTGAATTAATGCAATTTCGTCCGCATCTTTg                                                    >  2:129621/1‑140 (MQ=255)

                                                                                      cATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTCAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTGTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGtctc                                             <  1:342655/140‑1 (MQ=255)

                                                                                        ttttGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTa                                           <  1:546012/140‑1 (MQ=255)

                                                                                           tGCTTTCTAATATTGCCTGTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAAtt                                        <  2:259431/140‑1 (MQ=255)

                                                                                             gtttCTTATATGGCCGTTAATTCTTTGTCAGTGACGCCGTCTTTTACAAAAGTTAAAAGATATTGATATGTTTCAACAACAATATTAGCTGCTTTTTGAATTAAAGAAATTTTGTCAGCAGCTTTGACGTCTCTAAtttt                                      <  2:63959/139‑1 (MQ=255)

                                                                                                           cTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATGTGTTTTTGGAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAg                        <  1:126999/140‑1 (MQ=255)

                                                                                                                  tCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTCCAGTTTTAGAAATGCt                 >  2:254737/1‑140 (MQ=255)

                                                                                                                   cTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATCTCTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATCAGAAATGCtt                <  1:397977/140‑1 (MQ=255)

                                                                                                                   cTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCtt                >  2:468908/1‑140 (MQ=255)

                                                                                                                        taaGTCATGCCTCCTTTTACAACAGTTAAAATATATTCCTCTGTTTTATACCCAATTTCAGTTGATTAACCAATGAAAACAAGTACACCATCAACTTTGACGTCTCTAATTTTATCTACAGTATTAGCAATGCTTATTaa           >  1:108971/3‑140 (MQ=255)

                                                                                                                         cAGTCATGCCTCCTTGTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAAt          >  1:410876/1‑140 (MQ=255)

                                                                                                                          aGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATg         >  2:365091/1‑140 (MQ=255)

                                                                                                                          aGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTCGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATg         >  2:365120/1‑140 (MQ=255)

                                                                                                                            tCATGCCTCGTTTTACAACAGTTATAATTTATTCATATGTTTCATCAACAATATTTGTGAGCTGGTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGat       <  1:262205/140‑1 (MQ=255)

                                                                                                                             cATGCCTCCTTTTACAACAGTTAATATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATgttg      >  1:351030/1‑137 (MQ=255)

                                                                                                                                 cctcctTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGATATACg  <  1:451786/140‑1 (MQ=255)

TCACTTGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAATGATATACG  >  USA300TCH1516_ALE/1646057‑1646325

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A